Profiling of open chromatin in developing pig (Sus scrofa) muscle to identify regulatory regions

The landscape of chromatin accessibility in skeletal muscle during embryonic development in pigs

(2021) Jingwei Yue et al.   Journal of Animal Science and Biotechnology

Postnatal development of skeletal muscle in pigs with intrauterine growth restriction: morphofunctional phenotype and molecular mechanisms

(2020) Fernando Felicioni et al.   JOURNAL OF ANATOMY

Functional Annotation of the Transcriptome of the Pig, Sus scrofa, Based Upon Network Analysis of an RNAseq Transcriptional Atlas

(2020) Kim M. Summers et al.   Frontiers in Genetics

Low birth weight influences the postnatal abundance and characteristics of satellite cell subpopulations in pigs

(2020) K. Stange et al.   Scientific Reports

Systematic alteration of ATAC-seq for profiling open chromatin in cryopreserved nuclei preparations from livestock tissues

(2020) M. M. Halstead et al.   Scientific Reports

Genome-Wide Association Study and Fine Mapping Reveals Candidate Genes for Birth Weight of Yorkshire and Landrace Pigs

(2020) Yong Li et al.   Frontiers in Genetics

An improved pig reference genome sequence to enable pig genetics and genomics research

(2020) Amanda Warr et al.   GigaScience

A comparative analysis of chromatin accessibility in cattle, pig, and mouse tissues

(2020) Michelle M. Halstead et al.   BMC GENOMICS

Chromatin remodeling in bovine embryos indicates species-specific regulation of genome activation

(2020) Michelle M. Halstead et al.   Nature Communications

An integrated chromatin accessibility and transcriptome landscape of human pre-implantation embryos

(2019) Longqi Liu et al.   Nature Communications

Genome-Wide Identification of Histone Modifications Involved in Placental Development in Pigs

(2019) Kun Han et al.   Frontiers in Genetics

JASPAR 2020: update of the open-access database of transcription factor binding profiles

(2019) Oriol Fornes et al.   NUCLEIC ACIDS RESEARCH

A functional regulatory variant of MYH3 influences muscle fiber-type composition and intramuscular fat content in pigs

(2019) In-Cheol Cho et al.   PLoS Genetics

Multi-species annotation of transcriptome and chromatin structure in domesticated animals

(2019) Sylvain Foissac et al.   BMC BIOLOGY

ATACseqQC: a Bioconductor package for post-alignment quality assessment of ATAC-seq data

(2018) Jianhong Ou et al.   BMC GENOMICS

The myostatin gene: an overview of mechanisms of action and its relevance to livestock animals

(2018) D. Aiello et al.   ANIMAL GENETICS

Chromatin analysis in human early development reveals epigenetic transition during ZGA

(2018) Jingyi Wu et al.   NATURE

Associations between fetal size, sex and both proliferation and apoptosis at the porcine feto-maternal interface

(2018) Claire Stenhouse et al.   PLACENTA

FAANG, establishing metadata standards, validation and best practices for the farmed and companion animal community

(2018) P. W. Harrison et al.   ANIMAL GENETICS

Functional Annotation of Animal Genomes (FAANG): Current Achievements and Roadmap

(2018) Elisabetta Giuffra et al.   Annual Review of Animal Biosciences

Regulation of Muscle Growth in Early Postnatal Life in a Swine Model

(2018) Marko Rudar et al.   Annual Review of Animal Biosciences

Effects of parity and litter size on cortisol measures in commercially housed sows and their offspring

(2018) Sanne Roelofs et al.   PHYSIOLOGY & BEHAVIOR

TRIENNIAL GROWTH AND DEVELOPMENT SYMPOSIUM: Genetics and breeding for intramuscular fat and oleic acid content in pigs1

(2017) J. Estany et al.   JOURNAL OF ANIMAL SCIENCE

An improved ATAC-seq protocol reduces background and enables interrogation of frozen tissues

(2017) M Ryan Corces et al.   NATURE METHODS

The Encyclopedia of DNA elements (ENCODE): data portal update

(2017) Carrie A Davis et al.   NUCLEIC ACIDS RESEARCH

Identification of differentially expressed genes in longissimus muscle of pigs with high and low intramuscular fat content using RNA sequencing

(2016) K. S. Lim et al.   ANIMAL GENETICS

MultiQC: summarize analysis results for multiple tools and samples in a single report

(2016) Philip Ewels et al.   BIOINFORMATICS

Genetic determinants of pig birth weight variability

(2016) Xuemin Wang et al.   BMC GENETICS

Promotion of alleles by genome editing in livestock breeding programmes

(2016) J.M. Hickey et al.   JOURNAL OF ANIMAL BREEDING AND GENETICS

Near-optimal probabilistic RNA-seq quantification

(2016) Nicolas L Bray et al.   NATURE BIOTECHNOLOGY

deepTools2: a next generation web server for deep-sequencing data analysis

(2016) Fidel Ramírez et al.   NUCLEIC ACIDS RESEARCH

Developmental Stage, Muscle and Genetic Type Modify Muscle Transcriptome in Pigs: Effects on Gene Expression and Regulatory Factors Involved in Growth and Metabolism

(2016) Miriam Ayuso et al.   PLoS One

ChIPseeker: an R/Bioconductor package for ChIP peak annotation, comparison and visualization

(2015) Guangchuang Yu et al.   BIOINFORMATICS

Dynamic transcriptome profiles of skeletal muscle tissue across 11 developmental stages for both Tongcheng and Yorkshire pigs

(2015) Yuqiang Zhao et al.   BMC GENOMICS

Epigenomic Landscape of Human Fetal Brain, Heart, and Liver

(2015) Liying Yan et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The Genetic and Mechanistic Basis for Variation in Gene Regulation

(2015) Athma A. Pai et al.   PLoS Genetics

Discovery of Transcription Factors and Regulatory Regions Driving In Vivo Tumor Development by ATAC-seq and FAIRE-seq Open Chromatin Profiling

(2015) Kristofer Davie et al.   PLoS Genetics

Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

(2015) Leif Andersson et al.   GENOME BIOLOGY

Lean and obese pig breeds exhibit differences in prenatal gene expression profiles of muscle development

(2014) X. R. Yang et al.   Animal

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Effect of average litter weight in pigs on growth performance, carcass characteristics and meat quality of the offspring as depending on birth weight

(2013) C. E. Pardo et al.   Animal

Transposition of native chromatin for fast and sensitive epigenomic profiling of open chromatin, DNA-binding proteins and nucleosome position

(2013) Jason D Buenrostro et al.   NATURE METHODS

A gene expression atlas of the domestic pig

(2012) Tom C Freeman et al.   BMC BIOLOGY

The accessible chromatin landscape of the human genome

(2012) Robert E. Thurman et al.   NATURE

CCAAT-enhancer-binding protein-beta expression in vivo is associated with muscle strength

(2011) Lorna W. Harries et al.   AGING CELL

A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data

(2011) H. Li   BIOINFORMATICS

Comparative Analyses by Sequencing of Transcriptomes during Skeletal Muscle Development between Pig Breeds Differing in Muscle Growth Rate and Fatness

(2011) Xiao Zhao et al.   PLoS One

BEDTools: a flexible suite of utilities for comparing genomic features

(2010) Aaron R. Quinlan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Polybrominated diphenyl ethers (PBDEs) in free-range domestic fowl from an e-waste recycling site in South China: Levels, profile and human dietary exposure

(2008) Xiao-Jun Luo et al.   ENVIRONMENT INTERNATIONAL